Ed's Big Plans

Computing for Science and Awesome

iGEM: Freedom Unhashed

with 2 comments

An iGEM modeling meeting was held yesterday wherein Andre revealed his big plans for switching the team into enduserhood. Unfortunately, I didn’t follow along as well as I could have this time around and can really only document and comment on the bottom line.

We’ve again self-organized into two to three teams based on task. The first team is charged with creating a hashing function which creates a sequence of integrase usable tokens from an integer. The second (and third?) team is responsible for creating a check to ensure that a given product corresponds correctly to a given pair of reactant sequences. Finally, the dangling task of creating an even bigger external harness along with modifications to the present main.py program logic is likely being handled by the latter team.

The Hashing Task is kind of interesting because it essentially calls for unhashing an integer into a meaningful sequence rather than hashing a meaningful sequence into a unique integer. Since the reactant strings can themselves be lexicographically sequenced, then the task quickly becomes an enumeration or counting problem whereupon we find the most efficient way to count through the possible permutations of reactant tokens until we reach the integer that we want. The backward task (what we’re doing) may end up being implemented as the forward task with a sequential search.

The hashing subteam is headed by Jordan, the modeling head from last year and is joined by myself and Wylee– I honestly don’t see this as a task that can’t be completed by one person in a single bout of insanity– so it’s likely that I’ll hop over to Andre’s reactant-product verification team whenever this finishes.

We’ve planned another meeting for Tuesday 5pm next week to pull whatever we have together and to tackle any nascent problems.

Reactant-Product Verification is I think the more straight forward item, at least to explain. It is likely more technically challenging. Basically, we make the reaction go forward, and if the product matches what we wanted, then we favour the persistence of the product. … Err, at least that’s how I understood it… I’ll probably need to pop in and ask about it on Thursday before the big oGEM Skype meeting.

Side note– Oddly, both Shira and John were present at this meeting– it probably means we’re expecting progress πŸ˜€

Eddie Ma

July 22nd, 2009 at 5:36 pm

Matt says...

I’d actually like to see a bit more “current product verification” — that is, verifying that the code we currently have actually works — before moving on to the distributed-computing-and-madness realm.

That aside, I’m glad you figured out the hashing stuff. Just out of curiosity, what exactly is an open-form, lexicographically sequenced, permuted, time-amortized, mathematical expression that falls under counting problems, anyway? πŸ˜›

Eddie Ma says...

Okay, I accept your challenge: It is exactly as it sounds. Although I’m certain it didn’t sound *that* terrible when I said it πŸ˜›

Current product verification? Of course.